Biogenic fuel gas generation in geologic hydrocarbon deposits

ABSTRACT

A method of increasing biogenic production of a combustible gas from a subterranean geologic formation is described. The method may include extracting formation water from the geologic formation, where the extracted formation water includes at least a first species and a second species of microorganism. The method may also include analyzing the extracted formation water to identify the first species of microorganism that promotes the biogenic production of the combustible gas. An amendment may be introduced to the formation water to promote the growth of the first species of microorganism, and the biological characteristics of the formation water may be altered to decrease a population of the second species in the geologic formation.

CROSS REFERENCES TO RELATED APPLICATIONS

This application is a continuation of prior application Ser. No.13/607,909, filed Sep. 10, 2012, which is a continuation of priorapplication Ser. No. 13/173,140, filed Jun. 30, 2011, which is acontinuation of prior application Ser. No. 12/840,909, filed Jul. 21,2010, which is a continuation of prior application Ser. No. 12/129,441,filed May 29, 2008, which was a continuation of prior application Ser.No. 11/343,429, filed Jan. 30, 2006, which was a continuation-in-part ofInternational Application PCT/US2005/015259, with an internationalfiling date of May 3, 2005. The entire contents of all theabove-described applications are hereby incorporated by this referencefor all purposes.

FIELD OF THE INVENTION

The present invention relates to methods of rearranging the constituentpopulation of a native consortium of microorganisms to stimulate thegrowth of consortium members that produce metabolic products such ashydrogen and methane. Rearranging the constituents of the consortium mayinclude diluting the consortium microorganisms with formation waterextracted and transported from the geologic formation. It may alsoinclude introducing amendments to the native consortium that causes achange in the distribution of metabolic pathways and/or populationdistributions of consortium members.

BACKGROUND OF THE INVENTION

The formation water present in subterranean geologic formations of oil,coal, and other carbonaceous materials is normally considered anobstacle to the recovery of materials from those formations. In coalmining, for example, formation water often has to be pumped out of theformation and into remote ponds to make the coal accessible to miningequipment. Similarly, formation water has to be separated from the crudeoil extracted from a subterranean field and disposed of typicallyunderground. The extraction, separation and disposal of the formationwater add costs to recovery processes, and generate a by-productregarded as having little value.

Further investigation, however, has revealed that even extractedformation water can support active communities of microorganisms fromthe formation. The presence of these microorganism in the formationenvironment were known from previous recovery applications, such asmicrobially enhanced oil recovery (MEOR), where the microorganismsnaturally generate surface active agents, such as glycolipids, that helprelease oil trapped in porous substrates. In MEOR applications, however,it was generally believed that the microorganisms were concentrated in aboundary layer between the oil and water phases. The bulk formationwater was believed to be relatively unpopulated, because it lacked ahydrocarbon food source for the microorganisms. More recent studies haveshown that robust populations of microorganisms do exist in the bulkformation water, and can even survive extraction from the geologicformation under proper conditions.

The discovery of active populations of microorganisms in bulk formationwater has come at a time when new applications are being envisioned forthese microorganisms. For years, energy producers have seen evidencethat materials like methane are being produced biogenically informations, presumably by microorganisms metabolizing carbonaceoussubstrates. Until recently, these observations have been little morethan an academic curiosity, as commercial production efforts havefocused mainly on the recovery of coal, oil, and other fossil fuels.However, as supplies of easily recoverable natural gas and oil continueto dwindle, and interest grows using more environmentally friendly fuelslike hydrogen and methane, biogenic production methods for producingthese fuels are starting to receive increased attention.

Unfortunately, the techniques and infrastructure that have beendeveloped over the past century for energy production (e.g., oil and gasdrilling, coal mining, etc.) may not be easily adaptable tocommercial-scale, biogenic fuel production. Conventional methods andsystems for extracting formation water from a subterranean formationhave focused on getting the water out quickly, and at the lowest cost.Little consideration has been given to extracting the water in ways thatpreserve the microorganisms living in the water. Similarly, there hasbeen little development of methods and systems to harness microbiallyactive formation water for enhancing biogenic production of hydrogen,methane, and other metabolic products of the microbial digestion ofcarbonaceous substrates. Thus, there is a need for new methods andsystems of extracting, treating, and transporting formation waterwithin, between, and/or back into geologic formations, such thatmicrobial activity in the water can be preserved and even enhanced.

New techniques are also needed for stimulating microorganisms to producemore biogenic gases. Native consortia of hydrocarbon consumingmicroorganisms usually include many different species that can employmany different metabolic pathways. If the environment of a consortium ischanged in the right way, it may be possible to change the relativepopulations of the consortium members to favor more combustible gasproduction. It may also be possible to influence the preferred metabolicpathways of the consortium members to favor combustible gases as themetabolic end products. Thus, there is also a need for processes thatcan change a formation environment to stimulate a consortium ofmicroorganisms to produce more combustible biogenic gases.

BRIEF SUMMARY OF THE INVENTION

Embodiments of the invention relate to methods to stimulate biogenicproduction of a metabolite with enhanced hydrogen content. The methodsmay include the steps of forming an opening in a geologic formation toprovide access to a consortium of microorganisms, and injecting waterinto the opening to disperse at least a portion of the consortium over alarger region of a hydrocarbon deposit. The method may also includemeasuring a change in the rate of production of the metabolite in theformation.

Embodiments of the invention may still further relate to pumping andextraction methods to stimulate the biogenic production of a metabolitewith enhanced hydrogen content. The methods may include forming anopening in a geologic formation to provide access to a native consortiumof microorganisms. The method may also include injecting a first portionof water into the opening to disperse at least a portion of theconsortium over a larger region of a hydrocarbon deposit, extractingformation fluids from the geologic formation following the waterinjection, and injecting a second portion of the water into the openingafter extraction. The methods may also include measuring a change in therate of production of the combustible gas in the formation.

Embodiments of the invention may also further include methods tostimulate biogenic production of a metabolite with enhanced hydrogencontent by changing the salinity level of water in a geologic formation.The methods may include measuring a salinity level of formation water ina geologic formation. The methods may also include forming an opening inthe formation to provide access to a consortium of microorganisms, andinjecting water into the opening to reduce the salinity level of theformation water in the formation. The methods may additionally includemeasuring a change in the rate of production of the metabolite in theformation.

Embodiments of the invention still further relate to processes forenhancing a consortium of microorganisms to make materials with enhancedhydrogen content from carbonaceous substrates in an anaerobicenvironment. The processes may include extracting formation water from ageologic formation, and removing at least a portion of an extractablematerial from the formation water to make amended formation water. Thisextractable material may include microorganisms that are filtered out ofwater. The processes may further include introducing the amendedformation water to the carbonaceous material.

Embodiments of the invention may also relate to processes for increasingbiogenic hydrocarbon production in a geologic formation containing acarbonaceous material. The processes may include extracting formationwater from the formation, and removing at least a portion of one or morehydrocarbons from the formation water to make amended formation water.Microorganisms in water may also be filtered and/or sterilized to makethe amended formation water. The processes may further includereintroducing the amended formation water to the geologic formation.

Embodiments of the invention may also further relate to processes fortransporting formation water between geologic formations. The processesmay include extracting the formation water from a first formation, andremoving at least a portion of a hydrocarbon from the formation water tomake amended formation water. Microorganisms in water may also befiltered and/or sterilized to make the amended formation water. Theprocesses may also include transporting the amended formation water to asecond geologic formation, and introducing the amended formation waterto the carbonaceous material in the second geologic formation.Microorganisms may also be extracted from the first formation andintroduced to the second formation with the amended formation water.

Additional embodiments and features are set forth in part in thedescription that follows, and in part will become apparent to thoseskilled in the art upon examination of the specification or may belearned by the practice of the invention. The features and advantages ofthe invention may be realized and attained by means of theinstrumentalities, combinations, and methods described in thespecification.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a flowchart illustrating a method of intraformation transportof formation water according to embodiments of the invention;

FIG. 2 is a flowchart illustrating a method of transporting of formationwater between formations (i.e., interformation transport) according toembodiments of the invention;

FIG. 3 shows a system for the transporting of formation water within aformation (i.e., intraformation transport) according to embodiments ofthe invention;

FIG. 4 shows a system for interformation transport of formation wateraccording to embodiments of the invention;

FIGS. 5A-B are flowcharts illustrating methods according to embodimentsof the invention of using water to stimulate biogenic gas production bya consortium of microorganisms;

FIGS. 6A-B are flowcharts illustrating methods according to embodimentsof the invention of controlling the salinity level of the water in ageologic formation; and

FIG. 7 is a plot of the percentage of methane in the headspace of asealed coal container over time for three levels of added formationwater.

DETAILED DESCRIPTION OF THE INVENTION

Methods of stimulating the production of biogenic metabolites withenhanced hydrogen content (e.g., combustible gases such as methane andhydrogen) by changing the makeup of a consortium of microorganisms aredescribed. The changes may be brought about by diluting a nativeconsortium in water to disperse consortium members over a larger regionof a geologic formation. The dispersion can create opportunities for themicroorganism to grow with less competition from consortium members thatdo not generate metabolites with enhanced hydrogen content. When themicroorganisms are spread out over a larger region of a carbonaceoussubstrate (e.g., a hydrocarbon deposit such as an oil or coal bed) themicroorganism that are most effective at utilizing the substrate as afood source are expected to grow at the fastest rates. In an anaerobicformation environment, those metabolic processes typically include theconversion of the substrate to biogenic gases such as hydrogen andmethane, among other gases, as well as acetate (e.g., acetic acid).Consequently, the dispersion of the consortium in water is expected toincrease population growth for those microorganism species that are moreefficient at converting hydrocarbon substrates into metabolic productshaving enhanced hydrogen content such as hydrogen and methane.

While the aqueous dispersion may favor the growth of the hydrocarbonmetabolizers over other consortium members, it may not have as great animpact on the favored metabolic pathways of the metabolizers. Forexample, a methanogenic microorganism may be able to convert thehydrocarbon substrate into either methane or acetate. Embodiments of theinvention also include methods of stressing the microorganism to favormetabolic pathways that produce a target metabolic product (e.g.,hydrogen, methane, etc.) over other products (e.g., acetate, ammonia,hydrogen sulfide, carbon dioxide etc.). These methods includeintroducing an amendment to the formation environment surrounding themicroorganism consortium that may have an effect on the metabolicpathways at least some of the consortium members favor. The amendmentmay include a metabolite (i.e., a chemical intermediary or product of ametabolic process) generated by some of the consortium members. Byconcentrating the consortium environment with the metabolite, theconsortium members may be influenced to favor a different metabolicpathway that does not produce even more of the metabolite.Alternatively, a rate limiting metabolite may be introduced thatnormally causes a bottleneck in a metabolic pathway. Introducing thisamendment to the consortium environment may stimulate more use of thepathway to consume the added metabolite.

The water used for the dilution and dispersion of the consortium maycome from a variety of sources. One source that may be in closeproximity to the formation is formation water. Systems and methods forthe transport of anaerobic formation water from a subterranean geologicformation are described. “Anaerobic” formation water is characterized ashaving little or no dissolved oxygen, in general no more than 4 mg/L,preferably less than 2 mg/L, most preferably less than 0.1 mg/L, asmeasured at 20 degrees C. and 760 mmHg barometric pressure. Duringapplication of the present invention, higher levels of dissolved oxygen,greater than 4 mg/L, can be tolerated without appreciably degradingmicroorganism performance, for limited times or in certain locationssuch as a surface layer in a storage or settling tank. Dissolved oxygencan be measured by well-known methods, such as by commercially-availableoxygen electrodes, or by the well-known Winkler reaction.

The formation water may be extracted and then reintroduced into the sameformation in an intraformation transport process, or introduced into adifferent formation in an intraformation transport process. Theformation water may be analyzed to determine the chemical composition ofthe water, and to ascertain whether microorganisms are present. Whenmicroorganisms are present, they may also be identified by genus and/orspecies.

The choice of formation water may be influenced by the content and/oractivity of the microorganism found in the water. For example, a firstformation having native formation water containing high concentrationsof a microorganism of interest may be transported to a second formationto attempt to stimulate the growth of the microorganism in the secondformation. The water transported to the new formation may contain apopulation of the microorganism, which may act as a seed population forthe growth of the microorganism in the second formation.

The formation water may be amended based on the analysis of thecompounds and microorganisms present in the native water. Theseamendments may include changing the composition of the formation waterto enhance the growth of one or more species of the microorganismspresent. For example, the amendments may include adjusting themicroorganism nutrient levels, pH, salinity, oxidation potential (Eh),and/or metal ion concentrations, among other compositional changes tothe formation water. The amendments may also include filtering and/orprocessing the formation water to reduce the concentration of one ormore chemical and/or biological species.

Amended or unamended, the extracted formation water is transported backto the same formation, or a different formation. For example,intraformation transport may include cycling the formation water throughthe formation one or more times, where the water may be extracted fromthe formation, amended, and returned to the formation in a continuousloop process. Interformation transport may include, for example,extracting formation water from a first formation and transporting it(treated or untreated) to a second subterranean formation that hascarbonaceous materials, but little or no native formation water and/ormicroorganisms. The aqueous environment introduced to the secondformation creates conditions for microorganism populations to grow andconvert the carbonaceous material into hydrogen, smaller hydrocarbons(e.g., butane, propane, methane), and other useful metabolites.

Referring now to FIG. 1, a flowchart is shown that illustrates a methodof intraformation transport of formation water according to embodimentsof the invention. The method starts with the accessing the formationwater 102 in a geologic formation. The geologic formation may be apreviously explored, carbonaceous material containing, subterraneanformation, such as a coal mine, oil field, natural gas deposit,carbonaceous shale, etc. In many of these instances, access to theformation water can involve utilizing previously mined or drilled accesspoints to the formation. For unexplored formations, accessing theformation water may involve digging, or drilling through a surface layerto access the underlying water.

Once the formation water is accessed, it may be extracted from theformation 104. The extraction may involve bringing the formation waterto the surface using one or more hydrologic pumping techniques. Thesetechniques may include pumping the formation water to the surface usinga pumping device that harnesses electrical, mechanical, hydraulic,pneumatic, and/or fluid-expansion type forces, among other modes ofaction.

The extracted formation water may be analyzed 106 to ascertaininformation about the chemical and biological composition of the water.Chemical analyses may include spectrophotometry, NMR, HPLC, gaschromatography, mass spectrometry, voltammetry, and otherinstrumentation and chemical tests. The tests may determine the presenceand concentrations of elements like carbon, phosphorous, nitrogen,sulfur, magnesium, manganese, iron, calcium, zinc, tungsten, andtitanium, among others. The tests may also detect the presence andconcentrations of polyatomic ions, such as PO₄ ²⁻, NH₄ ⁺, NO₂ ⁻, NO₃ ⁻,and SO₄ ⁻, among others. Biological analyses may include techniques andinstrumentation for detecting genera and/or species of one or moremicroorganisms present in the formation water. These test may includegenus and/or species identification of anaerobes, aerobes,microaerophiles, etc. found in the formation water. Additional detailsfor identifying and isolation genera and species of microorganisms fromthe formation water are described in commonly assigned U.S. patentapplication Ser. No. 11/099,879, filed Apr. 5, 2005, and titled “Systemsand Methods for the Isolation and Identification of Microorganisms fromHydrocarbon Deposits”, the entire contents of which are herebyincorporated by reference for all purposes.

The formation water may also be amended 108 by, for example, alteringone or more physical (e.g., temperature), chemical, or biologicalcharacteristics of the water. As noted above, the amendments may includeadjustments to the chemical composition of the formation water,including the increase or decrease of a microorganism nutrient level,pH, salinity, oxidation potential (Eh), and/or metal ion concentration,among other chemical species. For example, changes in microorganismnutrient levels may include changes in formation water concentration ofcationic species, such as ammonium, calcium, magnesium, sodium,potassium, iron, manganese, zinc, and copper, among other cationicspecies. It may also include changes in anionic species, such asnitrate, nitrite, chloride, carbonate, phosphate, acetate, andmolybdate, among other anionic species. It may further include changesin the nutrient level of compounds including di-sodium hydrogenphosphate, boric acid, yeast extract, peptone, and chelating compoundslike nitrilotriacetic acid, among other compounds.

Changes in the biological characteristics of the formation water mayinclude increasing or decreasing the population of one or more generaand/or species of microorganism in the water. Genera whose population inthe formation water may be controlled include, Thermotoga, Pseudomonas,Gelria, Clostridia, Moorella, Thermoacetogenium, Methanobacter,Bacillus, Geobacillus, Methanosarcina, Methanocorpusculum,Methanobrevibacter, Methanothermobacter, Methanolobus,Methanohalophilus, Methanococcoides, Methanosalsus, Methanosphaera,Granulicatella, Acinetobacter, Fervidobacterium, Anaerobaculum,Ralstonia, Sulfurospirullum, Acidovorax, Rikenella, Thermoanaeromonas,Desulfovibrio, Dechloromonas, Acetogenium, Desulfuromonas, Ferribacter,and Thiobacillus, among others. Additional description ofmicroorganisms, and consortia of microorganisms, that may be present andcontrolled in the formation water can be found in commonly assigned U.S.patent application Ser. No. 11/099,881, filed Apr. 5, 2005, and titled“Generation of materials with Enhanced Hydrogen Content from AnaerobicMicrobial Consortia”; and U.S. patent application Ser. No. 11/099,880,also filed Apr. 5, 2005, titled “Generation of Materials with EnhancedHydrogen Content from Microbial Consortia Including Thermotoga”, theentire contents of both applications hereby being incorporated byreference for all purposes.

Whether amended or not, the extracted formation water may bereintroduced back into the geologic formation 110. The formation watermay be reintroduced at or near the location where the water isextracted, or at a position remote from the extraction location. Theremote position may or may not be in fluid communication with theextraction location (e.g., a cavity in the formation that ishydraulically sealed from the point where the formation water isextracted).

The formation water may be maintained in an anaerobic state during theextraction, pumping, transport, storage, etc., by using a closed systemthroughout and displacing the oxygen present in the system with an inertgas, such as argon, substantially pure nitrogen, and/or helium, amongother inert gases. The system may also be pressurized with the inert gasto reduce the amount of ambient oxygen that enters the system.Embodiments of anaerobic formation water extraction, transport andstorage systems may include low pressure pumps (e.g., vein, fin, and/orrotary pumps, which may use needle, ball and/or butterfly valves) thatmay be submersible in the subterranean formation water deposit. Theconduits and storage elements of the system may be made of oxygenimpermeable and chemically inert materials that minimize the diffusionof free oxygen and other contaminants into the anaerobic formationwater. Examples of these materials may include butyl rubber, viton,glass, copper, steel, and stainless steel, among other materials.

FIG. 2 shows another flowchart illustrating a method of interformationtransport of formation water according to embodiments of the invention.Similar to embodiments of methods of intraformation transport shown inFIG. 1, interformation transport may include accessing the formationwater 202 in a first geologic formation, and extracting the water 204from the first formation. The extracted formation water may be analyzed206, and amended 208 by altering one or more physical, chemical, and/orbiological characteristics of the water.

The formation water may then be transported to a second geologicformation 210. A variety of mechanisms are contemplated for transportingthe formation water between the two geologic formations. These includepumping the water through a pipeline that is in fluid communicationbetween the formations. They also include filling containers (e.g.,barrels) with formation water and transporting them by vehicle (e.g.,car, truck, rail car) to the second formation site. Alternatively, avehicle designed for the transport of fluids (e.g., a tanker truck,tanker rail car, etc.) may be filled with the formation water at thefirst formation site and driven (or pulled) to the second formationsite.

When the formation water arrives at the second formation site, it isintroduced into the second geologic formation 212. The second geologicformation may be a dry formation, where the formation water is pumpedinto a cavity, network of channels, etc. having little or no detectablelevels of native formation water. Alternatively, substantial amounts ofnative formation water may be present in the second formation, and thewater from the first formation is mixed with this native water as it isintroduced into the second formation.

FIG. 3 shows a system 300 for intraformation transport of formationwater according to embodiments of the invention. The system 300 mayinclude a pump system 302 and amendment system 304 that are positionedon the surface above a subterranean geologic formation 306. The geologicformation 306 may include a formation water stratum 308 that sits belowa liquid hydrocarbon layer 310 (e.g., a crude oil containing stratum),which, in turn, may sit below a gas layer 312 (e.g., a natural gaslayer). A conduit 314 may be inserted into the formation and positionedsuch that a distal end of the conduit 314 receives formation water fromthe stratum 308 and transports it to pump 302 on the surface. In someexamples, the conduit 314 may be part of a previous system used torecover hydrocarbons for the formation.

The pump system 302 used to bring the formation water to the surface mayinclude one or more pumping devices such as dynamic pumping devices,reciprocating displacement pumping devices, and rotary displacementpumping devices, among others.

Dynamic pumping devices may include centrifugal pumps, such as axialflow centrifugal pumps, mixed flow and/or radial flow pumps, peripheralpumps, and combinations of these pumps. Axial flow pumps may includesingle-stage or multi-stage, closed impeller, open impeller (e.g.,fixed-pitch or variable-pitch) and combinations of these pumps. Mixedflow and/or radial flow centrifugal pumps may include single suction ordouble suction, self-priming, non-priming, single-stage, or multi-stage,open-impeller, semiopen-impeller, closed-impeller, and combinations ofthese types of pumps. Peripheral centrifugal pumps may includesingle-stage or multi-stage, self-priming or non-priming, andcombinations of these types of pumps. Dynamic pumps may also include jetpumps, gas lift pumps, hydraulic ram pumps, and electromagnetic pumps,among other types of dynamic pumps.

Reciprocating displacement pumping devices may include piston or plungerpumps, including steam pumps (e.g., simplex, duplex, triplex ormultiplex steam pumps). These pumps may also include power pumps (e.g.,single-acting or double-acting; simplex, duplex, triplex, multiplex, andcombinations of these power pumps). Also included are pumps utilizingcheck valves, whether fixed, mobile, or a combination of thesecharacteristics, and may further include hinged barriers, mobile ballsor mobile pistons of appropriate shape, with associated containmentdevices. Also included in reciprocating displacement pumping devices arediaphragm pumps, including simplex, duplex and multiplex,fluid-operated, mechanically-operated, and combinations of these type ofpumps.

Rotary displacement pumping devices include pumps equipped with a singlerotor, including vane, piston, flexible member, screw and peristalticpumps. These pumps may also include pumps equipped with multiple rotors,including gear, lobe, circumferential piston, and screw pumps.

At least part of the pump system 302 may be submerged in a pool offormation water in a subterranean formation. In operation, the submergedpump may agitate the formation water, causing dissolved methane andother gases to be released and rise to the top of the formation. Thus,in some embodiments the pump system 302 may include a gas collectionsystem (not shown) at the well head to transport the released gases outof the formation.

When formation water exits the pump system 302 it may be transported toan amendment system 304 where the water may be analyzed and/or amendedbefore being reintroduced back into the formation 306. The analysiscomponents of the system 304 may include chemical and biologicalmeasurement instrumentation (not shown) used to provide data on thechemical and biological composition of the formation water. The system304 may also include components and equipment to change the physical,chemical and biological composition of the formation water. For example,the system 304 may include components to increase or decrease thetemperature of the water. The system may also include components andequipment to filter the formation water to remove selected chemicaland/or biological species. Descriptions of systems and method forfiltering formation water can be found in co-assigned PCT PatentApplication No. PCT/US2005/015188, filed May 3, 2005, and titled“Methanogenesis Stimulated by Isolated Anaerobic Consortia”, the entirecontents of which is hereby incorporated reference for all purposes. Theamendment system 304 may also include components for increasing ordecreasing a microorganism nutrient level, pH, salinity, oxidationpotential (Eh), and/or metal ion concentration, among other chemicalchanges to the water.

Formation water passing through the pump system 302 and the amendmentsystem 304 may then be transported thorough the pipeline 315 back intothe formation 306. In the embodiment shown, the formation water isreintroduced into the same formation water layer 308, but at a differentpoint from where the water was originally extracted. Alternatively, theformation water may be introduced back into the formation at anotherlayer, such as where an end of the conduit 316 opens to the gas layer312.

Referring now to FIG. 4, a system 400 for interformation transport offormation water according to embodiments of the invention is shown. TheSystem 400 include a pump system 402 and an amendment system 404positioned above a first geologic formation 406. Formation water may beextracted by pump system 402 from a formation water layer 408 throughthe conduit 414, and analyzed and amended in amendment system 404. Theamended formation water may then be loaded into the vehicle 418 whichcan travel between the first formation 406 and the second geologicformation 420.

When the vehicle 418 is filled with formation water it can travel topumping system 422 positioned above the second formation 420. An outlet(not shown) on the vehicle 418 may be connected to the pump unit 422 andthe formation water may be delivered to a subterranean cavity 424 abovea hydrocarbon bed 426, in the second formation 420, via conduit 428. Inalternative embodiments (not shown) the vehicle 418 may include pumpingequipment on-board to pump the formation water into the cavity 424,without the use of an on-site pumping system 422. In more alternativeembodiments, the vehicle 418 may be replaced by a transport pipeline(not shown) that transports the formation water directly between thefirst and second formations 408 and 420.

The extracted formation water may be used to disperse the constituentsof a native consortium over a larger region of carbonaceous material.The aqueous dispersion provides an opportunity for the upstreammetabolizers (e.g., the “first-bite” microorganisms that metabolize thehydrocarbon substrate into smaller molecules) and methanogenicmicroorganisms in the consortium to grow with less interference fromnearby competing species that are flushed from the hydrocarbon deposit.When conditions in the formation environment are favorable to rapidgrowth of the dispersed upstream metabolizers and methanogens, therelative populations of species in the consortium may become moreweighted to these consortium populations. Thus, diluting an originalconsortium (e.g., a native consortium) with water may change thedemographics of the microorganism members to increase the production ofbiogenic gases such as methane and hydrogen.

FIGS. 5A-B show flowcharts that illustrate methods of using water tostimulate biogenic gas production by a consortium of microorganisms. Themethod steps illustrated in FIG. 5A include forming an opening in ageologic formation 502 so water can be supplied to the microorganismconsortium. The opening may be formed under conditions that limit theamount of atmospheric oxygen that flows into the opening. Formation ofthe opening may include boring, drilling, digging, blasting, excavating,etc., the opening starting at the surface of the formation. Embodimentsalso include unplugging or otherwise accessing a opening that hasalready been formed in the formation (e.g., a previously drilled oilwell).

Following the formation of the opening, water may be injected into theopening 504. The water may have been extracted from the same formation,or have come from a different source, for example a different formation.The injected water may include live microorganisms, or the water may betreated to remove or inactivate the microorganisms. Removal treatmentsmay include passing the water through a filter that collects themicroorganisms in the retentate. Inactivation treatments may includeheating and/or irradiating the water to kill the microorganisms present.Inactivation treatments may also include adding a biocide to the waterto kill the microorganisms.

The water injected into the opening may disperse the consortium ofmicroorganisms over a larger region of the formation 506. For example,if the consortium is concentrated in a specific region of a hydrocarbondeposit (e.g., a coal or oil deposit), the water may disperse theconsortium over a larger region of the same deposit. The water may alsodilute the consortium in a larger volume of fluid.

The rate of gas production may be measured 508 to determine the effectof injecting the water. Measured gases may include hydrogen, methane,carbon monoxide, and/or carbon dioxide, among other gases. The type ofmeasurement may include a pressure measurement of the gases in theformation. This may involve partial pressure measurements of aparticular gas (or group of gases), like the combustible gases methaneand/or hydrogen. Measurements may be done before the water injection toestablish a baseline rate of off-gassing in the formation. Additionalmeasurements may be taken after the water injection to observe if therate of gas production has changed as a result of the injection.

The water injection may be as simple as injecting a single sample intothe opening. Embodiments may also include more complex patterns of waterinjection, where multiple cycles of water injection and extraction offluids from the formation are performed. FIG. 5B shows a water injectionpattern that includes the injection of two portions of water between anextraction step. Similar to FIG. 5A, the method may include forming anopening in a geologic formation 510 and injecting a first portion ofwater into the opening 512. A vacuum or some other type pressuredifferential may be applied to the opening to extract formation fluidsfrom the opening 514. Following the extraction, a second portion ofwater may be injected into the opening 516. Measurement of the gasproduction rates 518 may be taken before, during and after the waterinjection cycle to determine how the injected water is affecting gasproduction rates in the formation.

It should be appreciated that the injection-extraction-injection cycleshown in FIG. 5B may include more iterations. It should also beappreciated that the volume of the water injected and the timing of theinjection may be varied. For example, a first injection pattern mayinvolve several injection cycles of smaller volumes of water, while asecond pattern may involve fewer injection cycles of larger volumes ofwater.

Water injections and water treatments may also be done to change thesalinity level of water in geologic formation. FIG. 6A shows steps inmethods of controlling the salinity level of the water in a geologicformation according to embodiments of the invention. The methods mayinclude measuring the salinity level in the formation water 602. If thesalinity of the water is about 6% salt, by volume, or more (e.g.,brackish or saline water) then some microorganisms in the formationenvironment may have reduced activity due to the high saltconcentration. When the measured salinity level is high enough tointerfere with the desired microorganism activity, an opening may beformed in the formation 604 that provides access for a water dilutionamendment. Water having a reduced salinity level may be injected intothe formation 608 through the opening. During the water injection, thesalinity level of the in situ formation water may be monitored toquantify the impact of the water dilution. The salinity level in theformation water may continue to be monitored after the water injectionto see if the salinity level starts to rise again. Measurements ofmetabolite production rates, such as production rates for hydrogen,methane, carbon monoxide, acetate, etc., may also be conducted 608 togauge the impact of the reduced salinity level on biogenic activity.

The desired salinity level in a geologic formation depends in part onthe microorganism consortium. Some native or introduced consortia aremore active metabolizing carbonaceous substrates to metabolites withincreased hydrogen content when the salinity level is about 6% or less.Some microorganism see further increases in activity when salinitylevels reach about 3% or less. Some reach their highest activity levelsat even lower salinity levels, such as a level approaching what isconsidered fresh water (i.e., less than about 0.05% salt, by volume).Embodiments of the invention include increasing, as well as decreasing,the salinity level of water in the formation to reach a desired salinitylevel. For example, if the salinity level of the water is too low, saltamendments may be introduced (e.g., sodium chloride, potassium chloride,etc.) to increase the salinity.

The water injected into the geological formation to change the salinitylevel of the water into the formation may come from an external source,or the formation itself. FIG. 6B is a flowchart illustrating steps inmethods of changing the salinity by extracting, treating, andreintroducing water into same formation. The methods may includeaccessing the formation water in the geologic formation 652, andextracting a portion of the formation water 654. The salinity level of asample of the extracted formation water is measured 656 to see if thewater contains too much salt for significant metabolic production ofcarbon compound with enhanced hydrogen content.

If the salinity levels in the native formation water are too high, theextracted water may be treated to reduce the salinity level 658. Areduction in the salinity level of the water may be carried out by avariety of desalinization methods, including evaporation-condensationprocesses, multi-stage flash processes, electrodialysis reversalprocesses, reverse osmosis processes, freezing processes, andnanofiltration processes, among other processes. The desalinizationprocess may reduce the salt concentration in the formation water to thelevel of fresh water (e.g, 0.05% or less salt, by volume), or end athigher salinity levels (e.g., about 2% salt, by vol., or less).

The reduced salinity formation water may then be reintroduced back intothe geologic formation 658. Changes in the in situ salinity levels inthe formation may be monitored during and after the reintroduction ofthe treated water. Concentrations and/or production rates for metabolitespecies in the formation (e.g., hydrogen, methane) may also be measured.

Embodiments of the invention also include extracting, desalinating, andreintroducing formation water to a geologic formation in anuninterrupted cycle. Thus, a first portion of native formation water maybe extracted from the formation as a second portion is undergoing adesalinization process, and a third portion of treated water is beingreintroduced to the formation, all at the same time. As additionalcycles are completed, the salinity level of the formation water shouldbe further reduced.

DEFINITION OF SALINITY

Salinity is a measure of the dissolved salt concentration in water. Thesalts may include the dissolved ions of any ionic compounds present inthe water. Common salts may include halide salts such as alkali metalhalides (e.g., sodium chloride, potassium chloride, etc.) and alkaliearth metal halides (e.g., magnesium chloride, calcium chloride, etc.).Salts may also include the salts of polyatomic cations and anions, suchas ammonium salts, phosphate salts, nitrate salts, sulfate salts, andoxyhalide salts, among other kinds of salts.

The salinity level of “fresh water” is defined to have less than 0.05%,by vol, of salt. “Brackish water” has about 3% to 5% salt, by volume.“Brine” is defined as a concentrated salt solution that may be fullysaturated at room temperature with one of more dissolved salt compound.

EXPERIMENTAL

Laboratory experiments were done to measure how changes in the levels offormation water can effect methane production from coal extracted underanaerobic conditions from a subterranean coal seam. Formation water wasalso recovered from the formation under anaerobic conditions (i.e., theformation water samples were not exposed to ambient air).

Three coal samples of coal were taken from the Dietz Coal seam (NorthWest quadrant of the Powder River Basin). All three samples wereseparately placed in 125 ml serum bottles that were sealed in ananaerobic environment of argon gas. No formation water was added to thefirst sample bottle, while 0.2 ml of formation water was injected intothe second sample bottle, and 2.0 ml of formation water is injected intothe third sample bottle. The percentage of methane measured in theheadspace above the coal in the bottles was then measured over a 1 yearperiod. FIG. 7 shows the plot of the percentage of methane in theheadspace of the bottles over time for the three samples.

FIG. 7 clearly demonstrates that the addition of formation waterstimulates the production of methane from the coal samples. Additionalradiocarbon labeling studies provided strong evidence that the methanewas being biogenically produced. Thus, this experiment shows thatformation water can stimulate the biogenic production of methane fromcarbonaceous substrates like coal.

The Experiment shows that the addition of the formation water increasedthe percentage of methane nearly three-fold in about 150 days. Thepresent invention contemplates systems and methods for amending andtransporting formation water to carbonaceous materials in formations oncommercial scales. A proportional scaling of the resulting increase inmethane production will make these formations, which include dormant oiland coal fields, commercially viable sources of methane, hydrogen, andother metabolites from the microbial digestion of carbonaceoussubstrates.

Additional experiments are proposed to measure the effects of consortiumdilution and metabolite amendments on the production of biogenic gases.These include a first set of experiments for injecting water into ageologic formation containing coal. The coal deposit is an “active” coalthat has been shown to produce methane from either biogenic processes(e.g., methanogenic microorganisms) or non-biogenic processes (e.g.,methane desorption off the substrate, thermal breakdown of substrate,etc.). The water may be fresh water or salt water that has been filteredof microorganisms. This set of experiments compares changes in the rateof methane and hydrogen off-gassing based on how the water is introducedto the coal. For example, in one experiment, larger volumes of water areinjected at higher pressure in fewer cycles, while a second experimentinjects smaller volumes at lower pressure in more cycles. In these “huffand puff” experiments, fluids building up in the formation may also beextracted from between injection events. The measurements of the changesin the rates at which methane, hydrogen and other gases are building upin the formation offer insight into how a consortium of nativemicroorganisms responds to the different patterns for water injectionand extraction cycles.

A second set of experiments compares changes in the rate of methane andhydrogen off-gassing after introducing water to both active and inactivecoals. The active coals demonstrated significant methane off-gassingprior to introducing the water, while the inactive coals showed verylittle pre-water off-gassing. The water used in these experiments isextracted from the formation itself and the native microorganism are notfiltered or killed. In some experiments, the formation water may beextracted from the part of the formation in contact with the coal, whilein others the water is taken from a different part of the formation.Different patterns of water injection cycles may also be compared forboth the active and coal coals in this set of experiments.

A third set of experiments measures the effect of specific nutrientamendments on the rate of off-gassing from a deposit of active coal in ageologic formation. The nutrient amendments are added to water that'sinjected into the formation and onto the coal. The amendments mayinclude a high concentration of yeast extract, a low concentration ofyeast extract and phosphorous in various combinations. The water usedcomes for the formation. The same injection pattern is used forintroducing the amended water to the coal to better attribute andcorrelate differences in off-gassing rates to the type of amendmentused.

A fourth set of experiments introduces microorganism concentrates to aninactive coal deposit and measures changes in the off-gassing of gasessuch as hydrogen and methane. The microorganism concentrate may comefrom the retentate of filtered formation water. The experiments may usedifferent injection patterns to introduce the microorganisms to thecoal. The experiments may also dilute the concentrate to various levels(e.g., diluting the concentrate to 50%, 25%, 10%, etc., of its originalconcentration) to measure the effects of this dilution on theconcentrate's ability to stimulate biogenic gas production.

A fifth set of experiments introduces hydrogen gas to the coals andmeasures its effect on the rate of off-gassing of methane. Theexperiments include introducing the hydrogen gas to both active andinactive coals. The hydrogen gas may be introduced after water has beenintroduced to the coals. In some of the experiments, microorganisms mayalso be introduced to the coal before its exposed to the hydrogen gas,or simultaneously therewith. Nutrient amendments, such as vitamins,minerals, yeast extract, phosphorous, phosphate, etc., may also beadded.

A sixth set of experiments introduces acetate to the coals and measuresits effect on the rate of off-gassing from the coal. The acetate may beintroduced as an aqueous solution of acetic acid that's injected intothe formation and onto the coal. Similar to the hydrogen gasexperiments, the acetate experiments may be conducted on both active andinactive coals. Some of the experiments may include introducingmicroorganisms to the coal as well.

Tables 1A and B lists some of the experimental parameters for the sixsets of experiments described above. It should be appreciated that thelist in Tables 1A and B are not exhaustive, and different combinationsof parameters (as well and additional parameters) may also be tried.

TABLE 1A Experimental Parameters for Six Sets of Experiments Cells CellsCell Experimental Treatment Cells In Grown Nutrient Water FilteredConcentrate Set Summary Treatment on Surface Addition Source Out AddedFirst Fresh Water Formation No None Any Water Yes No First Fresh WaterFormation No None Any Water Yes No Second Water Flush Formation No NoneSame Well None No Second Water Flush Formation No None Same Well None NoSecond Water Flush Formation No None Same None No Formation Second WaterFlush Formation No None Same None No Formation Third NutritionalFormation & No High YE Same None No Water Formation Third NutritionalFormation & No Low YE Same None No Water Formation Third NutritionalFormation & No P Same None No Water Formation Third NutritionalFormation & No High YE + P Same None No Water Formation ThirdNutritional Formation & No Low YE + P Same None No Water FormationFourth Inoculation Cell Conc. No Low MMV Specific to Yes Yes CellsFourth Inoculation Cell Conc. No Low MMV Specific to Yes Yes CellsFourth Grow and Cell Conc. No Low MMV Any Water Yes Yes - Diluted DliuteFifth H₂ Add Formation No Low MMV Same Well Yes No Formation Fifth H₂Add Formation & No Low MMV Same Well No No Both Water Fifth H₂ Add WaterYes Low MMV Same No No Water Formation Fifth H₂ Add Water Yes Low MMVAny Water Yes Yes New Cells Sixth Acetate Add Formation No Low MMV SameWell Yes No Sixth Acetate Add Formation & No Low MMV Same Well No NoWater Sixth Acetate Add Water Yes Low MMV Same No No Formation SixthAcetate Add Water Yes Low MMV Any Water Yes Yes

TABLE 1-B Experimental Parameters for Six Sets of Experiments (con't)Number Big or Water Experi- of Small High Level Water Number mentalInjection Injection or Low Over Active Wash of Set Cycles VolumePressure Coal Coal First? Wells First Several Small Low No Yes N/A FewFirst Few Big High No Yes N/A Several Second Several Small Low No Yes NoSeveral Second Few Big High No No No Several Second Several Small Low NoYes No Few Second Few Big High No No No Several Third Few Big High NoYes No Several Third Few Big High No Yes No Several Third Few Big HighNo Yes No Several Third Few Big High No Yes No Several Third Few BigHigh No Yes No Several Fourth Several Small Low No No Maybe Few FourthFew Big High No No Maybe Several Fourth Several Small Low No No Yes FewFifth Several Small Low Yes Yes Maybe Few Fifth Several Small Low Yes NoMaybe Few Fifth Several Small Low No No Yes Few Fifth Several Small LowNo No Yes Few Sixth Several Small Low No Yes Maybe Few Sixth SeveralSmall Low No No Maybe Few Sixth Several Small Low No No Yes Few SixthSeveral Small Low No No Yes Few

In Tables 1A-B the nutrient addition “MMV” indicates metals, mineralsand/or vitamin amendment was made; “YE” indicates a yeast extractamendment was made; and “P” indicates phosphate amendment was made.

Examples of mineral amendments may include the addition of chloride,ammonium, phosphate, sodium, magnesium, potassium, and/or calcium to theisolate, among other kinds of minerals. Metal amendments may include theaddition of manganese, iron, cobalt, zinc, copper, nickel, selenate,tungstenate, and/or molybdate to the isolate, among other kinds ofmetals. Vitamin amendments may include the addition of pyridoxine,thiamine, riboflavin, calcium pantothenate, thioctic acid,p-aminobenzoic acid, nicotinic acid, vitamin B12,2-mercaptoehanesulfonic acid, biotin, and/or folic acid, among othervitamins. The addition of these amendments may involve adding mineralsalts, metal salts, and vitamins directly to the isolate, or firstpreparing a solution of the salts and vitamins that then gets added tothe isolate.

The concentration of the MMV, YE and P amendments may depend on theconcentration and composition of an isolated consortium. Examples ofconcentration ranges for amendment components may include about 1 mg/Lto about 500 mg/L for mineral amendment; about 10 μg/L to about 2000μg/L for a metal amendment; and about 1 μg/L to about 100 μg/L for avitamin amendment.

Having described several embodiments, it will be recognized by those ofskill in the art that various modifications, alternative constructions,and equivalents may be used without departing from the spirit of theinvention. Additionally, a number of well known processes and elementshave not been described in order to avoid unnecessarily obscuring thepresent invention. Accordingly, the above description should not betaken as limiting the scope of the invention.

Where a range of values is provided, it is understood that eachintervening value, to the tenth of the unit of the lower limit unlessthe context clearly dictates otherwise, between the upper and lowerlimits of that range is also specifically disclosed. Each smaller rangebetween any stated value or intervening value in a stated range and anyother stated or intervening value in that stated range is encompassed.The upper and lower limits of these smaller ranges may independently beincluded or excluded in the range, and each range where either, neitheror both limits are included in the smaller ranges is also encompassedwithin the invention, subject to any specifically excluded limit in thestated range. Where the stated range includes one or both of the limits,ranges excluding either or both of those included limits are alsoincluded.

As used herein and in the appended claims, the singular forms “a”, “an”,and “the” include plural referents unless the context clearly dictatesotherwise. Thus, for example, reference to “a process” includes aplurality of such processes and reference to “the electrode” includesreference to one or more electrodes and equivalents thereof known tothose skilled in the art, and so forth.

Also, the words “comprise,” “comprising,” “include,” “including,” and“includes” when used in this specification and in the following claimsare intended to specify the presence of stated features, integers,components, or steps, but they do not preclude the presence or additionof one or more other features, integers, components, steps, acts, orgroups.

1.-10. (canceled)
 11. A method of preparing a microbial community foruse in a geologic formation, the method comprising: forming an openingin a geologic formation to provide access to a consortium ofmicroorganisms; extracting at least a portion of a hydrocarbon substratefrom the geologic formation, wherein the extraction maintains thehydrocarbon substrate under anaerobic conditions; identifying one ormore microorganisms within the hydrocarbon substrate; and developing anex situ consortium comprising the one or more microorganisms identified.12. The method of claim 11, further comprising extracting formationwater from the geologic formation with the hydrocarbon substrate. 13.The method of claim 11, wherein the hydrocarbon substrate includes oneor more materials selected from the group consisting of coal, oil,kerogen, peat, lignite, oil shale, tar sands, bitumen, and tar.
 14. Themethod of claim 11, further comprising providing a nutrient amendment tostimulate growth of the consortium.
 15. The method of claim 11, furthercomprising isolating one or more microorganisms from the consortium. 16.The method of claim 11, measuring a rate of a biogenic hydrocarbonproduction of the hydrocarbon substrate from the developed consortium.17. The method of claim 11, further comprising anaerobically filteringthe extracted portion of the hydrocarbon substrate to concentrateincluded microorganisms.
 18. The method of claim 11, wherein theidentification comprises the detection of genetic material.
 19. Themethod of claim 11, wherein the identification comprises the detectionof proteins or portions of proteins expressed by the microorganisms. 20.The method of claim 11, wherein the ex situ consortium comprises amethanogen.
 21. The method of claim 11, wherein the ex situ consortiumcomprises one or more syntrophs.
 22. The method of claim 11, wherein theex situ consortium comprises one or more microorganisms that convert thehydrocarbon substrate into components including a carboxylate functionalgroup.
 23. A method of preparing an ex situ microbial community, themethod comprising: extracting at least a portion of a hydrocarbonsubstrate from a geologic formation, wherein the extraction maintainsthe hydrocarbon substrate under anaerobic conditions; detecting DNA forone or more microorganisms within the hydrocarbon substrate; purifyingDNA for the one or more microorganisms within the hydrocarbon substrate;and developing an ex situ consortium comprising the one or moremicroorganisms.
 24. The method of claim 23, further comprisingamplifying the amount of DNA.
 25. The method of claim 23, wherein thehydrocarbon substrate includes one or more materials selected from thegroup consisting of coal, oil, kerogen, peat, lignite, oil shale, tarsands, bitumen, and tar.
 26. The method of claim 23, further comprisingdesorbing the microorganisms from the hydrocarbon substrate prior to theDNA detection.
 27. The method of claim 26, wherein the desorptioncomprises using an anaerobic buffer.
 28. The method of claim 23,measuring a rate of a biogenic hydrocarbon production of the hydrocarbonsubstrate from the developed consortium.
 29. The method of claim 23,further comprising anaerobically filtering the extracted portion of thehydrocarbon substrate to concentrate included microorganisms.
 30. Themethod of claim 23, wherein the ex situ consortium comprises amethanogen.